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1,582 results for “manuscript”
Python code generating the data of figures 2, 3, 4, 5 and 6 of the manuscript: The evolution of cooperation in the unidirectional linear division of labour of finite roles
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Hiding in plain sight: The biomolecular identification of pinniped use in medieval manuscripts – MALDI and mtDNA data set
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All simulation results, figures and code regarding the manuscript: Calibrating models of cancer invasion: parameter estimation using Approximate Bayesian Computation and gradient matching
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Dataset associated with the manuscript: Soil management legacy interacts with wheat genotype to determine access to organic N in a dryland system
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Data to support manuscript "Fates and fingerprints of sulfur and carbon following wildfire in economically important croplands of California, U.S."
Abstract Sulfur (S) is widely used in agriculture, yet little is known about its fates within upland watersheds, particularly in combination with disturbances like wildfire. This dataset includes samples collected within the Napa River Watershed, California, U.S., where high S applications to vineyards are common, and ~20% of the watershed burned in October 2017. The data package includes soil, soil leachate, and stream chemistry data from sites representing a combination of land use (vineyard agriculture and grasslands) and burn (burned and unburned). Bulk soil chemical measurements include total sulfur and carbon concentrations and sulfur stable isotopes. We then used a laboratory rainfall experiment to simulate a wet season of precipitation in order to compare unburned and low severity burned vineyard and grassland soil leachate chemistry. Soil leachate measurements include total dissolved sulfur, sulfate, and dissolved organic carbon concentrations, sulfate-sulfur stable isotopes, and the specific ultraviolet absorbance at 254 nm (SUVA254), an index strongly correlated with DOC aromaticity. We compared soil leachate chemistry to stream samples draining sub-catchments with differing land use and degrees of burn and severity to understand combined effects at broader spatial scales. Soil and stream chemistry are provided in separate data tables, and data from the laboratory rainfall experiment is included in the leachingexpts (leaching experimental record), leachingexpchem (chemistry), and leachingexpisotopes (sulfur stable isotopes) data tables.
Supplementary material for the manuscript: Genetic structure of the European hedgehog (Erinaceus europaeus) in Denmark
<p>This database contains supplementary material for our manuscript "Genetic structure of the European hedgehog (<em>Erinaceus europaeus</em>) in Denmark":</p> <p><strong>S1 Fig/Figure 1a.</strong> Box plot of the individual heterozygosity (iH<sub>O</sub>) estimated for the six populations</p> <p><strong>S2 Fig/Figure 1b. </strong>Plot of the iH<sub>O</sub> values ranked from the lowest to the highest values within each population</p> <p><strong>S3 Fig/Figure 2. </strong>Likelihood plot of STRUCTURE results</p> <p><strong>S4 Fig/Figure 3.</strong> Likelihood plot of STRUCTURE results (for separate populations)</p> <p><strong>S5 Fig/Figure 4. </strong>Principal Component Analysis</p> <p><strong>S1 Table/Table 2. </strong>Overview of individuals for genetic sampling</p> <p><strong>S2 Table/Table 3. </strong>Dataset from GENEPOP</p> <p><strong>S3 Table/ Table 4. </strong>Data for fragmentation analyses</p> <p><strong>S4 Table/Table 1.</strong> Tukey’s test matrix for testing pairwise significant differences of the mean iH<sub>O</sub> between the six populations</p>
DATA for manuscript entitled "Integrating Transcriptomes and Somatic Mutations to Identify RNA Methylation Regulators as a Prognostic Marker in Hepatocellular Carcinomas"
<p><strong>Raw data of TCGA dataset and 7-meta data.</strong></p>
Data in support of manuscript submitted to JGR-Planets "Strong variability of Martian water ice clouds during dust storms revealed from ExoMars Trace Gas Orbiter/NOMAD"
<p>These files contain data underlying figures for the submission version of:</p> <p>Strong variability of Martian water ice clouds during dust storms revealed from ExoMars Trace Gas Orbiter/NOMAD</p> <p>which was submitted to JGR: Planets for review. </p> <p>The access to the dataset will be closed until the final version of the paper is accepted.</p>
Supplement of manuscript 521330
<p>This folder contains analysis data from the study submitted as manuscript (Manuscript ID 521330):</p> <p>TITLE:</p> <p>Comparative metabarcoding and metatranscriptomic analysis of microeukaryotes within coastal surface waters of West Greenland and Northwest Iceland</p> <p>AUTHORS:</p> <p>Stephanie Elferink, <a href="mailto:Stephanie.westphal@awi.de"> Stephanie.westphal@awi.de</a>, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research<sup> </sup> </p> <p>Sylke Wohlrab, <a href="mailto:Sylke.wohlrab@awi.de"> Sylke.wohlrab@awi.de</a>, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, and Helmholtz Institute for Functional Marine Biodiversity<sup> </sup></p> <p>Stefan Neuhaus, <a href="mailto:Stephan.neuhaus@awi.de">Stephan.neuhaus@awi.de</a>, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research<sup> </sup> </p> <p>Allan Cembella, <a href="mailto:Allan.Cembella@awi.de"> Allan.Cembella@awi.de</a>, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research<sup> </sup> </p> <p>Lars Harms, <a href="mailto:Lars.Harms@awi.de"> Lars.Harms@awi.de</a>, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, and Helmholtz Institute for Functional Marine Biodiversity<sup> </sup></p> <p>Uwe John, <a href="mailto:Uwe.John@awi.de"> Uwe.John@awi.de</a>, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, and Helmholtz Institute for Functional Marine Biodiversity</p> <p>JOURNAL:</p> <p>Frontiers in Marine Science, section Marine Molecular Biology and Ecology</p> <p>MS-ID:</p> <p>521330</p> <p>HOWTO:</p> <p>Sequences identified as Alveloates or Stramenopiles (description in manuscript) had been were classified more accurately by PhyloAssigner version 6.166 (https://github.com/jungbluth/phyloassigner, Vergin et al., 2013, DOI:10.1038/ismej.2013.32) with a phylogenetic placement onto reference trees based on 18S/28S concatenated alignments, according to Elferink et al. 2017 (DOI: 10.1016/j.dsr.2016.11.002).</p> <p>CONTENT:</p> <p>reference databases:</p> <p>- Alveolata_SSU-LSU-concat_310715_636.phyloassignerdb</p> <p>- Stramenopiles_SSU_LSU_concat_030815_1777.phyloassignerdb</p> <p>query sequence files:</p> <p>- Alveolata_seqtab_SIGN_dada2.fasta</p> <p>- Alveolata_seqtab_SIGN_dada2.fasta</p> <p>created out put folder including the taxonomic annotation:</p> <p>- Alveolata_seqtab_SIGN_dada2.place.out</p> <p>- Stramenopiles_seqtab_SIGN_dada2.place.out</p> <p>text file containing the used commands:</p> <p>- commands</p> <p> </p> <p> </p> <p> </p> <p> </p>
Dataset of Synchrotron Low Energy XRF and STXM files used in a manuscript on "Compressive Sensing for Dynamic XRF Scanning"
<p>Synchrotron Low Energy XRF and STXM Dataset used in a research manuscript on "Compressive Sensing for Dynamic XRF Scanning". This dataset includes HDF5 files with XRF (/dante) and STXM (/andor) maps and metadata such as XRF lifetime and sample stage positions (/sample_motors). The dataset also includes as TIFF images various outputs such as the sparse maps, the masked areas and the results of in-painting methods. In the DAT file, there is the output of the fitted XRF data as ASCII from PyMCA. In HTML there is included the relevant part of the electronic logbook (DonkiLOG). These data were acquired during the beamtime experiments 20180178 and 20192072 in the <a href="http://www.elettra.eu/elettra-beamlines/twinmic.html">TwinMic</a> soft X-ray microscopy beamline of Elettra Sincrotrone Trieste.</p> <p> </p> <p> </p>
Supplementary Figures for the manuscript 'Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph' by Albergante et al.
<p>Multidimensional datapoint clouds representing large datasets are frequently characterized by non‐trivial low‐dimensional geometry and topology which can be recovered by unsupervised machine learning approaches, in particular, by principal graphs. Principal graphs approximate the multivariate data by a graph injected into the data space with some constraints imposed on the node mapping. Here we present ElPiGraph, a scalable and robust method for constructing principal graphs. ElPiGraph exploits and further develops the concept of elastic energy, the topological graph grammar approach, and a gradient descent‐like optimization of the<br> graph topology. The method is able to withstand high levels of noise and is capable of approximating data point clouds via principal graph ensembles. This strategy can be used to estimate the statistical significance of complex data features and to summarize them into a single consensus principal graph. ElPiGraph deals efficiently with large datasets in various fields such as biology, where it can be used for example with single‐cell transcriptomic or epigenomic datasets to infer gene expression dynamics and recover differentiation landscapes.</p> <p> </p>
Supplementary online material for PhD thesis manuscript Proteomic approaches to the characterization of tolerance and virulence in bacterial biofilms
<p>These data belong to a PhD thesis manuscript Proteomic approaches to the characterization of tolerance and virulence in bacterial biofilms.</p> <p> </p> <p><strong>Supplementary online material 1</strong></p> <p>Theoretical proteome of <em>Staphylococcus aureus </em>ATCC 25923.</p> <p><strong>Supplementary online material 2</strong></p> <p>Theoretical proteome of <em>Pseudomonas aeruginosa </em>PAO1.</p> <p><strong>Supplementary online material 3</strong></p> <p>MaxQuant (v. 1.6.1.0) output of exoproteomic analysis carried out on a dual-species biofilm model.</p> <p><strong>Supplementary online material 4</strong></p> <p>MaxQuant (v. 1.6.1.0) output of surfaceomic analysis carried out on a dual-species biofilm model</p> <p><strong>Supplementary online material 5</strong></p> <p>Curated MaxQuant (v. 1.6.1.0) output of exoproteomic analysis carried out on a dual-species biofilm model.</p> <p><strong>Supplementary online material 6</strong></p> <p>Curated MaxQuant (v. 1.6.1.0) output of surfaceomic analysis carried out on a dual-species biofilm model.</p> <p><strong>Supplementary online material 7</strong></p> <p>Protein quantification of valid identifications in LC-MS/MS analysis of <em>Staphylococcus aureus </em>and <em>Pseudomonas aeruginosa </em>dual-species biofilms.</p>
Neutron Reflectometry data and code for the manuscript entitled: 'Enrichment of charged monomers explains non-monotonic polymer volume fraction profiles of multi-stimulus responsive copolymer brushes'
<p>Contained in the zip file is the reduced neutron reflectometry data, the code used to analyse the data and jupyter notebooks used implement this code. Data is for proposal number PP4274, experiment number PPR6490 on the Platypus Reflectometer at ANSTO, Australia. The data is name with measurement numbers. The attached excel document describes the condition which corresponds to measurement number. </p>
Files corresponding to submitted manuscript "Seismically-induced unclogging in fluid-saturated faults"
<p>Submission version of files.</p>
The dataset of the manuscript "Numerical study of the initial condition and emission on simulating PM2.5 concentrations in Comprehensive Air Quality Model with extensions version 6.1 (CAMx v6.1): Taking Xi'an as example"
<ul> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/bcfile.rar?versionId=4909d094-5877-408e-bd4f-0c969c54e585">bcfile.rar</a>: the clean initial and boundary condition files.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/Emis_forNov.rar?versionId=0a1e8b66-5157-4819-8c03-20fb7797d8ef">Emis_forNov.rar</a> and <a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/Emis_forDec.rar?versionId=d4db00f1-ec1b-4096-973e-6a87133e4eac">Emis_forDec.rar</a>: the emission files in November and December 2016.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/tuvfile.rar?versionId=5dcf0977-e416-466e-9089-bbf0726c788d">tuvfile.rar</a> and <a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/o3mapfile.rar?versionId=9c25cae9-f00e-4ad3-b4dc-7a721f7f44d7">o3mapfile.rar</a>: the photolysis files.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/camx.cp1.rar?versionId=09ded31b-4c42-4e40-a21c-0f18877e9e41">camx.cp[1-5].rar</a>: the results of sensitivity experiments for using clean initial condition files.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/camx.r1120p1.rar?versionId=45d6e209-8e66-43ed-bc0b-dc8af5521352">camx.r1120p[1-3].rar</a>: the results of sensitivity experiments for R1120.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/camx.r1124.rar?versionId=c138e436-0416-4701-948d-ce761cf6c5cf">camx.r1124.rar</a>: the results of sensitivity experiments for R1124.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/contnuous_B12.rar?versionId=34485c43-77ac-4001-8a6d-a57b7ff821e3">contnuous_B12.rar</a>: the results of sensitivity experiments for CT12.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/contnuous_B24.rar?versionId=0f325a61-f19c-4bac-b8b4-7e229c332bf9">contnuous_B24.rar</a>: the results of sensitivity experiments for CT24.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/scripts.zip?versionId=b030444c-51a5-4673-b9d1-7e80ec42a3b9">scripts.zip</a>: all scripts covering every data processing action for all the results reported in the paper.</li> <li><a href="https://zenodo.org/api/files/cabf59e1-a955-4190-a83c-48d82efea4e6/data.zip?versionId=52917a53-fca7-4a72-ba2f-a2ce7593adc4">data.zip</a>: final data tables used to plot figures and tables.</li> </ul>
STEG data of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies
<p>Figure_7_data: laboratory data of TEG output power working at low temperature differences. Data used in Figure 7 of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies.</p> <p>Figure_9_data: experimental data of TEG temperature differences from July 24 to July 31, 2017. Data used in Figure 9 of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies.</p> <p>Figures_11_14_data: input and output data of the STEG model. One-year cycle data. Used to obtain figures 11 to 14 of manuscript "Electrical Generation of a Ground Level Solar Thermoelectric Generator: Experimental Tests and One-year Cycle Simulation" submitted to Energies</p>
The NMR dataset for manuscript nl-2020-017186
<p>The NMR dataset for the determination of enthalpy change and entropy change of CNT-polymer association</p>
Data set for the manuscript "Reproductive physiology corresponds to adult nutrition and task performance in a Neotropical paper wasp: a test of dominance-nutrition hypothesis predictions"
<p>Data set for the manuscript "Reproductive physiology corresponds to adult nutrition and task performance in a Neotropical paper wasp: a test of dominance-nutrition hypothesis predictions"</p>
supplementary video for the manuscript "Parallelized manipulation of adherent living cells by magnetic nanoparticles-mediated forces"
<pre><strong>Video S6: Parallelized magnetic control of Hela cells</strong></pre> <pre><strong>Video S7: Parallelized magnetic control of SHSY-5Y cells</strong></pre> <pre><strong>Video S8: Parallelized magnetic control of cortical neurons</strong></pre> <pre><strong>Video S9: Parallelized magnetic control of cortical neurons</strong></pre> <pre><strong>Video S10&S11: Parallelized magnetic control of PC12 cells</strong></pre> <pre><strong>Video S12: Lysosome labeling of Hela cells</strong></pre> <pre><strong>Video S13: Late endosome labeling of Hela cells</strong></pre>
Data associated with manuscript by Mousset et al
<p>Phenotypic data set and pedigree data associated with the manuscipt by Mousset et al. Genetic variation underlies the plastic response to shade of snapdragon plants (<em>Antirrhinum majus</em> L.). </p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.